A new partnership agreement between Waikato FC and the Waikato-Bay of Plenty Football Federation is going to secure the future of the region's national league side.

By the middle of next month the two entities will submit their application for a three-year premiership licence to New Zealand Football, with Waikato having been granted an extension on the December 16 deadline because of promising talks about changes to the franchise's governance model in partnership with the federation.

Waikato FC have been part of the national league since 2004, but their future was in doubt, as they struggled to maintain administrators, volunteer helpers and match supporters.

Their current licence, like all of the premiership teams, expires at the end of the season.

After a meeting between clubs on November 26, it was agreed the best way forward was a united approach, which will be led by the federation - the governing body.

"There's a number of benefits in terms of opening it up and actually having it as a more traditional sort of sports model, in terms of a provincial representation side, which is what we're accustomed to in New Zealand," Waikato-Bay of Plenty Football Federation CEO Cam Mitchell said.

The new franchise will be re-named WaiBOP United and Mitchell said it would operate 12 months of the year in a professional capacity and would provide better player and coach pathways and open up more potential commercial and funding opportunities.

The federation will assist with the day to day operations of the franchise, in a similar way that the region's women's national league team functions.

Other premiership teams are also run in similar ways.

Mitchell also wants this model to benefit the clubs, and get more of those players feeding into the franchise team.

Patsi Davies, chair of the Wai-BOP federation, said the presence of flagship youth and senior men's teams was an essential part of the player pathway in the region.

"The federation will look to build on WFC's good work in retaining a top level men's football team and a youth team in the ASB Premiership," she said. "Both teams are strategically important in offering a talent pathway for aspiring and current players in the Federation Talent Centre programme."

While Waikato FC and the federation got together in a similar way in 2010, that relationship lasted just half a year, when the parties agreed to part ways.